Rv3207c Still unknown · low auto-curated
H37Rv Rv3207c · MTBC0 - ·
285 aa · 3583801–3584658 (-) ·
RefSeq NP_217723.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3152. Function unknown. Foldseek best (non-significant) hit: 6n8l-assembly1_T Cryo-EM structure of early cytoplasmic-late (ECL) pre (prob 0.09, TM 0.41). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O05859
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | Zinc-dependent metalloprotease |
| Orthologous group | COG5479 |
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.442 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
DUF3152 | PF11350.15 | 1.4e-104 | 73–283 | Protein of unknown function (DUF3152) |
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 90.2 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
6n8l-assembly1_T |
0.09 | 0.41 | 9.3e+00 | 6n8l-assembly1_T Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribosomal subunit |
6hiw-assembly1_CI |
0.01 | 0.19 | 5.6e+00 | 6hiw-assembly1_CI Cryo-EM structure of the Trypanosoma brucei mitochondrial ribosome - This entry contains the complete small mitoribosomal subunit in complex with mt-IF-3 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1417 (membrane protein), medium confidence from genomic context alone (score 696 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3205c hyp |
hypothetical protein | 749 | 749 ctx | neighborhood:589 cooccurence:413 |
Rv1417 |
membrane protein | 707 | 696 ctx | cooccurence:692 |
Rv1698 mctB |
copper transporter MctB | 691 | 692 ctx | cooccurence:684 |
Rv3669 |
transmembrane protein | 691 | 691 ctx | cooccurence:691 |
Rv1083 hyp |
hypothetical protein | 645 | 646 ctx | cooccurence:644 |
Rv2980 hyp |
hypothetical protein | 637 | 637 ctx | cooccurence:637 |
Rv3206c moeB1 |
adenylyltransferase/sulfurtransferase MoeZ | 600 | 600 ctx | neighborhood:594 |
Rv3311 hyp |
hypothetical protein | 599 | 600 ctx | cooccurence:594 |
Rv0358 hyp |
hypothetical protein | 589 | 589 ctx | cooccurence:589 |
Rv1222 rseA |
anti-sigma E factor RseA | 579 | 579 ctx | cooccurence:574 |
Rv2520c |
membrane protein | 570 | 570 ctx | cooccurence:570 |
Rv3217c |
integral membrane protein | 562 | 562 ctx | cooccurence:560 |
Rv0556 |
transmembrane protein | 553 | 554 ctx | cooccurence:547 |
Rv1109c hyp |
hypothetical protein | 525 | 526 ctx | cooccurence:510 |
Rv3212 hyp |
hypothetical protein | 511 | 512 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): DUF3152 PF11350.15 (E=1e-104)
- Foldseek best: 6n8l-assembly1_T Cryo-EM structure of early cytoplasmic-late (ECL) pre-60S ribos (prob 0.09, E=9e+00, TM=0.41)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_217723.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3152 (PF11350.15)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
COG5479 - Curated reference: UniProt O05859 (TrEMBL, unreviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Model confidence: ESMFold per-residue pLDDT (mean 90.2, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
52 functional partner(s); context anchor
Rv1417 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3207c| MSTYGWRAYALPVLMVLTTVVVYQTVTGTSTPRPAAAQTVRDSPAIGVVGTAILDAPPRGLAVFDANLPAGTLPDGGPFTEAGDKTWRVVPGTTPQVGQGTVKVFRYTVEIENGLDPTMYGGDNAFAQMVDQTLTNPKGWTHNPQFAFVRIDSGKPDFRISLVSPTTVRGGCGYEFRLETSCYNPSFGGMDRQSRVFINEARWVRGAVPFEGDVGSYRQYVINHEVGHAIGYLRHEPCDQQGGLAPVMMQQTFSTSNDDAAKFDPDFVKADGKTCRFNPWPYPIP